Starting phenix.real_space_refine on Fri Feb 14 05:21:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674.map" model { file = "/net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jvh_36674/02_2025/8jvh_36674_neut.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6289 2.51 5 N 1599 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9699 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9699 Classifications: {'peptide': 1205} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 26, 'TRANS': 1178} Chain breaks: 6 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 5.36, per 1000 atoms: 0.55 Number of scatterers: 9699 At special positions: 0 Unit cell: (72.6, 119.9, 144.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1771 8.00 N 1599 7.00 C 6289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.28 Conformation dependent library (CDL) restraints added in 1.1 seconds 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 62.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 removed outlier: 3.645A pdb=" N GLU A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 37 removed outlier: 3.694A pdb=" N ARG A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 48 removed outlier: 3.622A pdb=" N LYS A 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 48 " --> pdb=" O PRO A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 48' Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.668A pdb=" N ALA A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 69 No H-bonds generated for 'chain 'A' and resid 67 through 69' Processing helix chain 'A' and resid 70 through 86 removed outlier: 3.823A pdb=" N SER A 76 " --> pdb=" O PRO A 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 137 removed outlier: 4.102A pdb=" N SER A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE A 101 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A 114 " --> pdb=" O MET A 110 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 removed outlier: 3.915A pdb=" N ASN A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 159 removed outlier: 4.017A pdb=" N ASP A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 170 removed outlier: 3.894A pdb=" N PHE A 170 " --> pdb=" O GLY A 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 167 through 170' Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.790A pdb=" N THR A 175 " --> pdb=" O ILE A 171 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N TYR A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 3.887A pdb=" N THR A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS A 197 " --> pdb=" O ARG A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 240 removed outlier: 3.975A pdb=" N LYS A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN A 219 " --> pdb=" O LYS A 215 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.858A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 303 removed outlier: 3.682A pdb=" N THR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N PHE A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N TYR A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS A 278 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N LEU A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 299 " --> pdb=" O TRP A 295 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 removed outlier: 3.681A pdb=" N SER A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 315 through 318' Processing helix chain 'A' and resid 319 through 334 removed outlier: 3.797A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET A 332 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 351 removed outlier: 3.565A pdb=" N ILE A 340 " --> pdb=" O ILE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 444 through 448 removed outlier: 3.552A pdb=" N ILE A 448 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 454 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.842A pdb=" N ILE A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 removed outlier: 3.894A pdb=" N LEU A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A 487 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N MET A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.697A pdb=" N VAL A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 539 " --> pdb=" O VAL A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 removed outlier: 3.775A pdb=" N LEU A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 579 removed outlier: 4.558A pdb=" N ARG A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 removed outlier: 3.688A pdb=" N GLU A 598 " --> pdb=" O ASP A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 694 removed outlier: 3.547A pdb=" N LEU A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 783 removed outlier: 3.837A pdb=" N ILE A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE A 783 " --> pdb=" O TYR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 803 removed outlier: 3.761A pdb=" N VAL A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR A 790 " --> pdb=" O LYS A 786 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 791 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE A 792 " --> pdb=" O ASP A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 815 removed outlier: 3.837A pdb=" N LEU A 808 " --> pdb=" O PRO A 804 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 815 " --> pdb=" O ALA A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 873 removed outlier: 3.746A pdb=" N ASN A 826 " --> pdb=" O ASN A 822 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE A 832 " --> pdb=" O ASN A 828 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR A 833 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE A 834 " --> pdb=" O TYR A 830 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 843 " --> pdb=" O ILE A 839 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ASN A 853 " --> pdb=" O ASN A 849 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 859 " --> pdb=" O ILE A 855 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG A 866 " --> pdb=" O THR A 862 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 872 " --> pdb=" O PHE A 868 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR A 873 " --> pdb=" O GLU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 881 removed outlier: 4.115A pdb=" N PHE A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN A 881 " --> pdb=" O SER A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 903 removed outlier: 4.001A pdb=" N ILE A 893 " --> pdb=" O LEU A 889 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 894 " --> pdb=" O SER A 890 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 897 " --> pdb=" O ILE A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 927 removed outlier: 5.210A pdb=" N VAL A 909 " --> pdb=" O VAL A 905 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 920 " --> pdb=" O MET A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 945 removed outlier: 3.768A pdb=" N ALA A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 934 " --> pdb=" O PRO A 930 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 963 removed outlier: 4.068A pdb=" N ILE A 959 " --> pdb=" O LYS A 955 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU A 960 " --> pdb=" O SER A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 991 removed outlier: 3.715A pdb=" N PHE A 990 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 986 through 991' Processing helix chain 'A' and resid 992 through 997 removed outlier: 3.783A pdb=" N VAL A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1014 Processing helix chain 'A' and resid 1016 through 1036 removed outlier: 4.364A pdb=" N ARG A1022 " --> pdb=" O LYS A1018 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A1029 " --> pdb=" O ILE A1025 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A1031 " --> pdb=" O ASN A1027 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A1033 " --> pdb=" O ALA A1029 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A1034 " --> pdb=" O LEU A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1037 through 1054 removed outlier: 4.006A pdb=" N LYS A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1081 removed outlier: 3.799A pdb=" N PHE A1068 " --> pdb=" O MET A1064 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A1070 " --> pdb=" O SER A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.998A pdb=" N ALA A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A1091 " --> pdb=" O SER A1087 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A1095 " --> pdb=" O LYS A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1175 Processing helix chain 'A' and resid 1240 through 1242 No H-bonds generated for 'chain 'A' and resid 1240 through 1242' Processing helix chain 'A' and resid 1264 through 1270 removed outlier: 3.532A pdb=" N LYS A1270 " --> pdb=" O TYR A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1288 removed outlier: 3.846A pdb=" N VAL A1281 " --> pdb=" O THR A1277 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1287 " --> pdb=" O ARG A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1293 through 1297 removed outlier: 3.928A pdb=" N LEU A1297 " --> pdb=" O ILE A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1303 removed outlier: 4.001A pdb=" N THR A1303 " --> pdb=" O LYS A1300 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1310 Processing helix chain 'A' and resid 1313 through 1327 removed outlier: 3.823A pdb=" N GLN A1318 " --> pdb=" O GLY A1314 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG A1319 " --> pdb=" O GLY A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1358 Processing helix chain 'A' and resid 1371 through 1378 removed outlier: 4.403A pdb=" N ARG A1377 " --> pdb=" O ALA A1373 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1417 Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 409 through 411 removed outlier: 4.016A pdb=" N ILE A 618 " --> pdb=" O TYR A 409 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460 removed outlier: 6.082A pdb=" N GLY A 458 " --> pdb=" O ILE A 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 635 through 636 removed outlier: 4.613A pdb=" N SER A 636 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 669 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1149 through 1151 removed outlier: 6.319A pdb=" N GLU A1231 " --> pdb=" O LYS A1129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1158 through 1161 removed outlier: 6.618A pdb=" N ALA A1158 " --> pdb=" O VAL A1382 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A1384 " --> pdb=" O ALA A1158 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A1160 " --> pdb=" O PHE A1384 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN A1385 " --> pdb=" O PHE A1393 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A1393 " --> pdb=" O ASN A1385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1251 through 1254 421 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3013 1.34 - 1.46: 1987 1.46 - 1.58: 4809 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 9876 Sorted by residual: bond pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 2.00e+00 bond pdb=" CG LEU A1080 " pdb=" CD2 LEU A1080 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.97e+00 bond pdb=" CA LEU A 362 " pdb=" C LEU A 362 " ideal model delta sigma weight residual 1.523 1.543 -0.021 1.49e-02 4.50e+03 1.92e+00 bond pdb=" C ILE A 328 " pdb=" N SER A 329 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.31e-02 5.83e+03 1.89e+00 bond pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.74e+00 ... (remaining 9871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 12969 2.02 - 4.03: 288 4.03 - 6.05: 41 6.05 - 8.07: 4 8.07 - 10.09: 3 Bond angle restraints: 13305 Sorted by residual: angle pdb=" C SER A1105 " pdb=" N ASN A1106 " pdb=" CA ASN A1106 " ideal model delta sigma weight residual 121.54 131.63 -10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C ASN A 440 " pdb=" N ASP A 441 " pdb=" CA ASP A 441 " ideal model delta sigma weight residual 121.54 128.60 -7.06 1.91e+00 2.74e-01 1.37e+01 angle pdb=" C ALA A 821 " pdb=" N ASN A 822 " pdb=" CA ASN A 822 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 angle pdb=" CA ASN A1106 " pdb=" CB ASN A1106 " pdb=" CG ASN A1106 " ideal model delta sigma weight residual 112.60 115.68 -3.08 1.00e+00 1.00e+00 9.50e+00 angle pdb=" C PRO A 361 " pdb=" N LEU A 362 " pdb=" CA LEU A 362 " ideal model delta sigma weight residual 123.91 128.78 -4.87 1.66e+00 3.63e-01 8.62e+00 ... (remaining 13300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5645 15.07 - 30.15: 274 30.15 - 45.22: 51 45.22 - 60.30: 1 60.30 - 75.37: 3 Dihedral angle restraints: 5974 sinusoidal: 2431 harmonic: 3543 Sorted by residual: dihedral pdb=" CA VAL A 905 " pdb=" C VAL A 905 " pdb=" N ASN A 906 " pdb=" CA ASN A 906 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA CYS A1151 " pdb=" C CYS A1151 " pdb=" N ASP A1152 " pdb=" CA ASP A1152 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA LYS A1016 " pdb=" C LYS A1016 " pdb=" N ASN A1017 " pdb=" CA ASN A1017 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 5971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 987 0.039 - 0.079: 401 0.079 - 0.118: 116 0.118 - 0.157: 22 0.157 - 0.196: 3 Chirality restraints: 1529 Sorted by residual: chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.84 -0.20 2.00e-01 2.50e+01 9.63e-01 chirality pdb=" CA ASN A1106 " pdb=" N ASN A1106 " pdb=" C ASN A1106 " pdb=" CB ASN A1106 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CA ASP A 441 " pdb=" N ASP A 441 " pdb=" C ASP A 441 " pdb=" CB ASP A 441 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 1526 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 437 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C ILE A 437 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE A 437 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE A 438 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1257 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A1258 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1258 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1258 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 440 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C ASN A 440 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN A 440 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP A 441 " -0.011 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 610 2.74 - 3.28: 10110 3.28 - 3.82: 13912 3.82 - 4.36: 17111 4.36 - 4.90: 29368 Nonbonded interactions: 71111 Sorted by model distance: nonbonded pdb=" O ILE A 286 " pdb=" OG SER A 289 " model vdw 2.195 3.040 nonbonded pdb=" O ILE A1375 " pdb=" OG SER A1378 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 144 " pdb=" OH TYR A 430 " model vdw 2.253 3.040 nonbonded pdb=" O PRO A 338 " pdb=" OG1 THR A 341 " model vdw 2.255 3.040 nonbonded pdb=" ND2 ASN A 774 " pdb=" OE1 GLU A1095 " model vdw 2.264 3.120 ... (remaining 71106 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9876 Z= 0.337 Angle : 0.785 10.087 13305 Z= 0.442 Chirality : 0.046 0.196 1529 Planarity : 0.004 0.050 1654 Dihedral : 9.557 75.370 3686 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 0.18 % Allowed : 2.21 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.19), residues: 1191 helix: -2.45 (0.16), residues: 713 sheet: -3.43 (0.53), residues: 56 loop : -3.61 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 186 HIS 0.011 0.002 HIS A 892 PHE 0.030 0.002 PHE A 294 TYR 0.027 0.002 TYR A 940 ARG 0.007 0.001 ARG A1176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 197 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 THR cc_start: 0.8516 (p) cc_final: 0.8294 (m) REVERT: A 153 SER cc_start: 0.8701 (t) cc_final: 0.8091 (p) REVERT: A 160 GLU cc_start: 0.7203 (pp20) cc_final: 0.6774 (pp20) REVERT: A 251 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7973 (mptt) REVERT: A 776 ARG cc_start: 0.6492 (ptp90) cc_final: 0.6186 (mmm-85) REVERT: A 924 MET cc_start: 0.8738 (ptt) cc_final: 0.8474 (ptt) REVERT: A 955 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8216 (ttpt) REVERT: A 1092 LEU cc_start: 0.8725 (tp) cc_final: 0.8468 (tp) outliers start: 2 outliers final: 0 residues processed: 197 average time/residue: 0.2941 time to fit residues: 75.8758 Evaluate side-chains 99 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 ASN A 894 ASN A 992 ASN A1256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.185696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.131481 restraints weight = 12888.495| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.93 r_work: 0.3554 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9876 Z= 0.196 Angle : 0.618 9.804 13305 Z= 0.324 Chirality : 0.043 0.167 1529 Planarity : 0.004 0.042 1654 Dihedral : 5.207 23.775 1301 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.56 % Allowed : 7.73 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.22), residues: 1191 helix: -1.32 (0.18), residues: 716 sheet: -2.93 (0.57), residues: 61 loop : -3.02 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1047 HIS 0.009 0.002 HIS A 676 PHE 0.015 0.001 PHE A 294 TYR 0.020 0.002 TYR A1266 ARG 0.005 0.001 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 153 SER cc_start: 0.8539 (t) cc_final: 0.7936 (p) REVERT: A 160 GLU cc_start: 0.7510 (pp20) cc_final: 0.7027 (pp20) REVERT: A 231 MET cc_start: 0.7972 (mtp) cc_final: 0.7656 (mtm) REVERT: A 251 LYS cc_start: 0.8419 (ttmm) cc_final: 0.7885 (mptt) REVERT: A 348 GLU cc_start: 0.7258 (pp20) cc_final: 0.6979 (pp20) REVERT: A 382 ASN cc_start: 0.6728 (m110) cc_final: 0.6171 (p0) REVERT: A 431 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6838 (t0) REVERT: A 776 ARG cc_start: 0.7001 (ptp90) cc_final: 0.6276 (mmm-85) REVERT: A 845 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8097 (mm-30) REVERT: A 897 VAL cc_start: 0.6858 (t) cc_final: 0.6632 (m) REVERT: A 1134 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7120 (ttm-80) REVERT: A 1256 GLN cc_start: 0.7406 (tp-100) cc_final: 0.6558 (mm110) outliers start: 17 outliers final: 11 residues processed: 131 average time/residue: 0.2451 time to fit residues: 44.2988 Evaluate side-chains 109 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1284 VAL Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.183528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128155 restraints weight = 13163.681| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.98 r_work: 0.3506 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9876 Z= 0.153 Angle : 0.542 9.340 13305 Z= 0.284 Chirality : 0.042 0.155 1529 Planarity : 0.003 0.041 1654 Dihedral : 4.712 22.460 1301 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.84 % Allowed : 8.92 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.23), residues: 1191 helix: -0.69 (0.19), residues: 719 sheet: -2.80 (0.58), residues: 71 loop : -2.73 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.005 0.001 HIS A1400 PHE 0.012 0.001 PHE A 633 TYR 0.016 0.001 TYR A 290 ARG 0.004 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7528 (pp20) cc_final: 0.7190 (pp20) REVERT: A 185 ILE cc_start: 0.8098 (tp) cc_final: 0.7813 (mp) REVERT: A 251 LYS cc_start: 0.8537 (ttmm) cc_final: 0.7995 (mptt) REVERT: A 382 ASN cc_start: 0.6799 (m110) cc_final: 0.6276 (p0) REVERT: A 582 LYS cc_start: 0.6350 (mttm) cc_final: 0.5955 (mtmm) REVERT: A 776 ARG cc_start: 0.7008 (ptp90) cc_final: 0.6454 (mmm160) REVERT: A 897 VAL cc_start: 0.6891 (t) cc_final: 0.6630 (m) REVERT: A 1249 ASN cc_start: 0.8885 (OUTLIER) cc_final: 0.8646 (t0) REVERT: A 1256 GLN cc_start: 0.7470 (tp-100) cc_final: 0.6583 (mm110) outliers start: 20 outliers final: 10 residues processed: 122 average time/residue: 0.2342 time to fit residues: 39.9977 Evaluate side-chains 104 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.176075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.118511 restraints weight = 13073.105| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.95 r_work: 0.3405 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9876 Z= 0.231 Angle : 0.596 8.814 13305 Z= 0.314 Chirality : 0.044 0.184 1529 Planarity : 0.004 0.045 1654 Dihedral : 4.785 22.450 1301 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.21 % Allowed : 9.75 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.23), residues: 1191 helix: -0.49 (0.19), residues: 726 sheet: -2.49 (0.60), residues: 71 loop : -2.73 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 186 HIS 0.006 0.001 HIS A1400 PHE 0.018 0.002 PHE A 842 TYR 0.018 0.002 TYR A 851 ARG 0.005 0.000 ARG A1134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7736 (pp20) cc_final: 0.7435 (pp20) REVERT: A 185 ILE cc_start: 0.8054 (tp) cc_final: 0.7788 (mp) REVERT: A 251 LYS cc_start: 0.8530 (ttmm) cc_final: 0.7913 (mptt) REVERT: A 382 ASN cc_start: 0.6780 (m110) cc_final: 0.6284 (p0) REVERT: A 776 ARG cc_start: 0.7021 (ptp90) cc_final: 0.6502 (mmm160) REVERT: A 1249 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8632 (t0) REVERT: A 1256 GLN cc_start: 0.7519 (tp-100) cc_final: 0.6583 (mm110) outliers start: 24 outliers final: 14 residues processed: 117 average time/residue: 0.2415 time to fit residues: 39.8720 Evaluate side-chains 104 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Chi-restraints excluded: chain A residue 1367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 30 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.113864 restraints weight = 13204.559| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.90 r_work: 0.3346 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9876 Z= 0.317 Angle : 0.633 8.578 13305 Z= 0.336 Chirality : 0.046 0.166 1529 Planarity : 0.004 0.047 1654 Dihedral : 5.015 23.976 1301 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.58 % Allowed : 11.41 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1191 helix: -0.60 (0.19), residues: 729 sheet: -2.33 (0.61), residues: 74 loop : -2.79 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 186 HIS 0.006 0.001 HIS A1400 PHE 0.021 0.002 PHE A 842 TYR 0.021 0.002 TYR A1097 ARG 0.004 0.001 ARG A1116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7880 (pp20) cc_final: 0.7537 (pp20) REVERT: A 185 ILE cc_start: 0.8017 (tp) cc_final: 0.7727 (mp) REVERT: A 231 MET cc_start: 0.8430 (mtm) cc_final: 0.8078 (mtm) REVERT: A 332 MET cc_start: 0.7619 (mmt) cc_final: 0.6848 (mmt) REVERT: A 382 ASN cc_start: 0.6808 (m110) cc_final: 0.6285 (p0) REVERT: A 431 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6854 (t0) REVERT: A 582 LYS cc_start: 0.6391 (mttm) cc_final: 0.6074 (mttp) REVERT: A 776 ARG cc_start: 0.7212 (ptp90) cc_final: 0.6750 (mmm160) REVERT: A 1134 ARG cc_start: 0.6955 (ttm-80) cc_final: 0.6574 (ttm-80) REVERT: A 1249 ASN cc_start: 0.8977 (OUTLIER) cc_final: 0.8637 (t0) REVERT: A 1256 GLN cc_start: 0.7630 (tp-100) cc_final: 0.6908 (tp40) REVERT: A 1376 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8157 (tmmt) outliers start: 28 outliers final: 13 residues processed: 114 average time/residue: 0.2349 time to fit residues: 37.5732 Evaluate side-chains 103 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 431 ASP Chi-restraints excluded: chain A residue 535 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.176829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.119096 restraints weight = 13206.755| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.96 r_work: 0.3402 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9876 Z= 0.151 Angle : 0.527 8.507 13305 Z= 0.279 Chirality : 0.042 0.204 1529 Planarity : 0.003 0.047 1654 Dihedral : 4.622 22.370 1301 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.47 % Allowed : 12.05 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.24), residues: 1191 helix: -0.16 (0.19), residues: 728 sheet: -2.20 (0.61), residues: 74 loop : -2.59 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.011 0.001 PHE A1170 TYR 0.015 0.001 TYR A 290 ARG 0.003 0.000 ARG A1116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7847 (pp20) cc_final: 0.7554 (pp20) REVERT: A 185 ILE cc_start: 0.7881 (tp) cc_final: 0.7643 (mp) REVERT: A 231 MET cc_start: 0.8441 (mtm) cc_final: 0.8083 (mtm) REVERT: A 239 MET cc_start: 0.8111 (tpp) cc_final: 0.7612 (tpp) REVERT: A 382 ASN cc_start: 0.6833 (m110) cc_final: 0.6306 (p0) REVERT: A 437 ILE cc_start: 0.7376 (mm) cc_final: 0.7120 (mm) REVERT: A 582 LYS cc_start: 0.6428 (mttm) cc_final: 0.6038 (mtmm) REVERT: A 776 ARG cc_start: 0.7014 (ptp90) cc_final: 0.6520 (mmm160) REVERT: A 1134 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6561 (ttm-80) REVERT: A 1249 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8519 (t0) REVERT: A 1256 GLN cc_start: 0.7591 (tp-100) cc_final: 0.6910 (tp40) REVERT: A 1376 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8164 (tmmt) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.2407 time to fit residues: 36.2691 Evaluate side-chains 102 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 919 LEU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 85 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.176120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.118203 restraints weight = 13219.904| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.99 r_work: 0.3399 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9876 Z= 0.159 Angle : 0.522 8.667 13305 Z= 0.276 Chirality : 0.042 0.180 1529 Planarity : 0.003 0.048 1654 Dihedral : 4.457 21.376 1301 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.47 % Allowed : 12.70 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1191 helix: 0.07 (0.19), residues: 728 sheet: -2.16 (0.61), residues: 74 loop : -2.51 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.014 0.001 PHE A 142 TYR 0.015 0.001 TYR A 290 ARG 0.008 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7929 (pp20) cc_final: 0.7665 (pp20) REVERT: A 185 ILE cc_start: 0.7863 (tp) cc_final: 0.7608 (mp) REVERT: A 231 MET cc_start: 0.8425 (mtm) cc_final: 0.8058 (mtm) REVERT: A 239 MET cc_start: 0.8135 (tpp) cc_final: 0.7612 (tpp) REVERT: A 332 MET cc_start: 0.7735 (mmt) cc_final: 0.6982 (mmt) REVERT: A 382 ASN cc_start: 0.6820 (m110) cc_final: 0.6301 (p0) REVERT: A 437 ILE cc_start: 0.7574 (mm) cc_final: 0.7245 (mm) REVERT: A 776 ARG cc_start: 0.7069 (ptp90) cc_final: 0.6557 (mmm160) REVERT: A 1134 ARG cc_start: 0.6812 (ttm-80) cc_final: 0.6547 (ttm-80) REVERT: A 1249 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8523 (t0) REVERT: A 1256 GLN cc_start: 0.7619 (tp-100) cc_final: 0.6964 (tp40) REVERT: A 1376 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8183 (tmmt) outliers start: 16 outliers final: 14 residues processed: 101 average time/residue: 0.2537 time to fit residues: 35.7516 Evaluate side-chains 101 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.0010 chunk 28 optimal weight: 2.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.177810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120131 restraints weight = 13250.778| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.02 r_work: 0.3408 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9876 Z= 0.130 Angle : 0.492 8.610 13305 Z= 0.260 Chirality : 0.041 0.174 1529 Planarity : 0.003 0.048 1654 Dihedral : 4.286 20.226 1301 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.56 % Allowed : 12.79 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.24), residues: 1191 helix: 0.29 (0.20), residues: 724 sheet: -2.15 (0.57), residues: 79 loop : -2.42 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 PHE 0.008 0.001 PHE A 78 TYR 0.015 0.001 TYR A 290 ARG 0.004 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8435 (mtm) cc_final: 0.8066 (mtm) REVERT: A 382 ASN cc_start: 0.6891 (m110) cc_final: 0.6384 (p0) REVERT: A 437 ILE cc_start: 0.7491 (mm) cc_final: 0.7174 (mm) REVERT: A 776 ARG cc_start: 0.7030 (ptp90) cc_final: 0.6516 (mmm160) REVERT: A 812 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7059 (mtp85) REVERT: A 1134 ARG cc_start: 0.6769 (ttm-80) cc_final: 0.6529 (ttm-80) REVERT: A 1249 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8474 (t0) REVERT: A 1256 GLN cc_start: 0.7588 (tp-100) cc_final: 0.6747 (mm110) REVERT: A 1376 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8187 (tmmt) outliers start: 17 outliers final: 13 residues processed: 110 average time/residue: 0.2642 time to fit residues: 39.8560 Evaluate side-chains 106 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.176828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.120648 restraints weight = 13103.295| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.15 r_work: 0.3390 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.4514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9876 Z= 0.152 Angle : 0.508 8.803 13305 Z= 0.268 Chirality : 0.041 0.161 1529 Planarity : 0.004 0.067 1654 Dihedral : 4.261 20.002 1301 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.66 % Allowed : 13.06 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.24), residues: 1191 helix: 0.40 (0.20), residues: 724 sheet: -2.26 (0.56), residues: 79 loop : -2.34 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.020 0.001 PHE A 411 TYR 0.015 0.001 TYR A 290 ARG 0.010 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8431 (mtm) cc_final: 0.8048 (mtm) REVERT: A 239 MET cc_start: 0.8017 (tpp) cc_final: 0.7515 (tpp) REVERT: A 382 ASN cc_start: 0.6931 (m110) cc_final: 0.6417 (p0) REVERT: A 409 TYR cc_start: 0.5443 (m-10) cc_final: 0.5095 (m-10) REVERT: A 776 ARG cc_start: 0.7049 (ptp90) cc_final: 0.6502 (mmm160) REVERT: A 812 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6895 (mtp85) REVERT: A 1134 ARG cc_start: 0.6653 (ttm-80) cc_final: 0.6416 (ttm-80) REVERT: A 1249 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8465 (t0) REVERT: A 1256 GLN cc_start: 0.7583 (tp-100) cc_final: 0.6943 (tp40) REVERT: A 1274 GLU cc_start: 0.8908 (pt0) cc_final: 0.8380 (mt-10) REVERT: A 1376 LYS cc_start: 0.8404 (mtpt) cc_final: 0.8153 (tmmt) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.2607 time to fit residues: 38.3793 Evaluate side-chains 103 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 89 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1070 PHE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 0.0770 chunk 63 optimal weight: 0.0020 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.5546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122435 restraints weight = 13231.227| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.19 r_work: 0.3412 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9876 Z= 0.130 Angle : 0.493 8.644 13305 Z= 0.259 Chirality : 0.041 0.168 1529 Planarity : 0.003 0.047 1654 Dihedral : 4.136 19.154 1301 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.56 % Allowed : 12.88 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1191 helix: 0.54 (0.20), residues: 732 sheet: -2.26 (0.57), residues: 79 loop : -2.30 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.004 0.001 HIS A1400 PHE 0.008 0.001 PHE A 78 TYR 0.015 0.001 TYR A 290 ARG 0.004 0.000 ARG A1283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2382 Ramachandran restraints generated. 1191 Oldfield, 0 Emsley, 1191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8436 (mtm) cc_final: 0.8051 (mtm) REVERT: A 239 MET cc_start: 0.7966 (tpp) cc_final: 0.7474 (tpp) REVERT: A 382 ASN cc_start: 0.6879 (m110) cc_final: 0.6330 (p0) REVERT: A 409 TYR cc_start: 0.5465 (m-10) cc_final: 0.5081 (m-10) REVERT: A 776 ARG cc_start: 0.7012 (ptp90) cc_final: 0.6461 (mmm160) REVERT: A 812 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6896 (mtp85) REVERT: A 1249 ASN cc_start: 0.8706 (OUTLIER) cc_final: 0.8426 (t0) REVERT: A 1256 GLN cc_start: 0.7540 (tp-100) cc_final: 0.6746 (mm110) REVERT: A 1274 GLU cc_start: 0.8840 (pt0) cc_final: 0.8296 (mt-10) REVERT: A 1376 LYS cc_start: 0.8412 (mtpt) cc_final: 0.8163 (tmmt) outliers start: 17 outliers final: 12 residues processed: 105 average time/residue: 0.2597 time to fit residues: 37.8052 Evaluate side-chains 104 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 812 ARG Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1025 ILE Chi-restraints excluded: chain A residue 1080 LEU Chi-restraints excluded: chain A residue 1088 GLU Chi-restraints excluded: chain A residue 1249 ASN Chi-restraints excluded: chain A residue 1263 MET Chi-restraints excluded: chain A residue 1294 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.175388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.116648 restraints weight = 13110.092| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.96 r_work: 0.3410 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9876 Z= 0.154 Angle : 0.504 8.767 13305 Z= 0.265 Chirality : 0.041 0.160 1529 Planarity : 0.003 0.047 1654 Dihedral : 4.163 18.939 1301 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.29 % Allowed : 13.16 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1191 helix: 0.55 (0.20), residues: 732 sheet: -2.33 (0.56), residues: 79 loop : -2.25 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1047 HIS 0.003 0.001 HIS A1400 PHE 0.010 0.001 PHE A1170 TYR 0.015 0.001 TYR A 290 ARG 0.003 0.000 ARG A1283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5107.71 seconds wall clock time: 91 minutes 35.81 seconds (5495.81 seconds total)